Experiment Overview
| Repository ID: | FR-FCM-Z3HK | Experiment name: | Simonds et al 2021 -- Figure 1a-c (CyTOF mass cytometry of human glioma, kidney cancer, sarcoma, PBMC) | MIFlowCyt score: | 24.00% |
| Primary researcher: | Erin Simonds | PI/manager: | Erin Simonds | Uploaded by: | Erin Simonds |
| Experiment dates: | 2018-04-01 - 2021-02-20 | Dataset uploaded: | Feb 2021 | Last updated: | Jun 2021 |
| Keywords: | None | Manuscripts: | |||
| Organizations: |
UCSF, San Francisco, (USA)
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| Purpose: | Immune profiles were obtained from 39 samples: 19 GBM primary tumor biopsies, 11 RCC primary tumor biopsies (one with paired tumor-adjacent normal tissue and metastatic lesion), 4 sarcoma primary tumor biopsies (one with paired tumor-adjacent normal tissue) and PBMCs from 1 healthy donor (with paired unstimulated and phytohemagglutinin-stimulated aliquots). Single-cell mass cytometry data were acquired using T cell-focused and myeloid-focused antibody panels with 42 markers each (see Materials & Methods and Suppl Tables S2 and S3). Data were filtered on CD45-positive cells and processed using the PhenoGraph + FlowSOM analysis pipeline ("PhenoSOM") to segregate immune cell types into metaclusters and quantify their frequency across samples. The cluster IDs after Step 2 of the PhenoSOM pipeline are attached as CSV files (compressed as ZIP files). A key to link the FCS filenames to the cluster ID CSV files are also attached. | ||||
| Conclusion: | Dataset from Simonds et al JITC 2021 (http://doi.org/10.1136/jitc-2020-002181) | ||||
| Comments: | Visit https://github.com/esimonds/PhenoSOM/wiki/Running-the-FR-FCM-Z3HK-demo for a tutorial on how to run PhenoSOM on the files in this experiment to obtain the plots in Figures 1A-1B of Simonds et al JITC 2021. | ||||
| Funding: | Not disclosed | ||||
| Quality control: | None | ||||
Experiment variables
| Sample Type | |
|---|---|
| · PrimaryTumor | FR-FCM-Z3HK - TcellPanel - glioma - COH001 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF10711 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF10941 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF10953 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF10985 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF10986 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11048 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11071 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11159 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11232 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11318A - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11331 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11378 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11447 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11496 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11503 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11512 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11517 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - glioma - SF11723 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - kidney - CIPSOCKID-010_T1 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - kidney - CIPSOCKID-01_T1 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - kidney - CIPSOCKID-05_T1 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - kidney - IPIKID-073 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - kidney - IPIKID-076 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - kidney - IPIKID-100 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - kidney - IPIKID-101 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - kidney - IPIKID-103 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - kidney - IPIKID-109_T1 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - kidney - IPIKID-111_T1 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - kidney - IPIKID-97_T1 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - sarcoma - IPISRC-013_T1 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - sarcoma - IPISRC-016 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - sarcoma - IPISRC-09 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - sarcoma - IPISRC-10 - Viable.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - COH001 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF10711 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF10941 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF10953 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF10985 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF10986 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11048 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11071 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11159 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11232 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11318A - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11331 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11378 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11447 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11496 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11503 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11512 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11517 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - glioma - SF11723 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - CIPSOCKID-010_T1 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - CIPSOCKID-01_T1 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - CIPSOCKID-05_T1 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - IPIKID-073 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - IPIKID-076 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - IPIKID-100 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - IPIKID-101 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - IPIKID-103 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - IPIKID-109_T1 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - IPIKID-111_T1 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - IPIKID-97_T1 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - sarcoma - IPISRC-013_T1 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - sarcoma - IPISRC-016 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - sarcoma - IPISRC-09 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - sarcoma - IPISRC-10 - Ungated.fcs |
| · PBMC | FR-FCM-Z3HK - TcellPanel - PBMC_PHA - HealthyDonor - Viable.fcs · FR-FCM-Z3HK - TcellPanel - PBMC_unstim - HealthyDonor - Viable.fcs · FR-FCM-Z3HK - MyeloidPanel - PBMC_PHA - HealthyDonor - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - PBMC_unstim - HealthyDonor - Ungated.fcs |
| · TumorAdjacentNormalTissue | FR-FCM-Z3HK - TcellPanel - kidney - CIPSOCKID-010_N1 - Viable.fcs · FR-FCM-Z3HK - TcellPanel - sarcoma - IPISRC-013_N1 - Viable.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - CIPSOCKID-010_N1 - Ungated.fcs · FR-FCM-Z3HK - MyeloidPanel - sarcoma - IPISRC-013_N1 - Ungated.fcs |
| · MetastaticTumor | FR-FCM-Z3HK - TcellPanel - kidney - CIPSOCKID-010_M1 - Viable.fcs · FR-FCM-Z3HK - MyeloidPanel - kidney - CIPSOCKID-010_M1 - Ungated.fcs |
